AVR32 Studio 1.0 and 2.0 as well as the GNU Toolchain 1.0 and 2.0 can co-exist. Therefore you may wait and uninstall the older versions when you are ready.
Simply install the AVR32 GNU Toolchain 2.0 first, then install AVR32 Studio 2.0 and start it. Every time AVR32 Studio starts it will test its environment and report errors if some required applications are missing. If you do not get any error messages you should be ready to go.
When upgrading AVR32 Studio from version 1.0 to 2.0 you have two choices with regards to your workspace. You can either upgrade your existing 1.0 workspace or you can create a new workspace and import your 1.0 projects.
If upgrading the workspace you should use a copy of your existing workspace. Changes will be made that will cause the upgraded workspace to be incompatible with AVR32 Studio 1.0.
AVR32 Studio 2.0 projects have quite different metadata compared to AVR32 Studio 1.0 projects and must thus be upgraded. Note that only projects that use the internal builder or the managed build system must be upgraded. Standard make projects will be left as they are.
It is also possible to import and upgrade individual projects: